Our final dataset comprised 200 molecules.

LLMs with improved chemical reasoning capabilities in the other two sub-tasks.

Genetic variants (GVs) are defined as differences in the DNA sequences among individuals and play a crucial role in diagnosing and treating genetic diseases. The rapid decrease in next generation sequencing cost, analogous to Moore's Law, has led to an exponential increase in the availability of patient-level GV data. This growth poses a challenge for clinicians who must efficiently prioritize patientspecific GVs and integrate them with existing genomic databases to inform patient management. To addressing the interpretation of GVs, genomic foundation models (GFMs) have emerged. However, these models lack standardized performance assessments, leading to considerable variability in model evaluations. This poses the question: How effectively do deep learning methods classify unknown GVs and align them with clinically-verified GVs? We argue that representation learning, which transforms raw data into meaningful feature spaces, is an effective approach for addressing both indexing and classification challenges. We introduce a large-scale genetic variant dataset, named GV-Rep, featuring variable-length contexts and detailed annotations, designed for deep learning models to learn GV representations across various traits, diseases, tissue types, and experimental contexts. Our contributions are three-fold: (i) Construction of a comprehensive dataset with 7 million records, each labeled with characteristics of the corresponding variants, alongside additional data from 17,548 gene knockout tests across 1,107 cell types, 1,808 variant combinations, and 156 unique clinically-verified GVs from real-world patients.

Previous work has investigated this problem under either full-information loss feedback with unknown transitions (Zhao et al., 2024), or bandit

Colloquially speaking, image generation models based upon diffusion processes are frequently said to exhibit "hallucinations"--samples that could never occur in the training data. But where do such hallucinations come from? In this paper, we study a particular failure mode in diffusion models, which we term mode interpolation. Specifically, we find that diffusion models smoothly "interpolate" between nearby data modes in the training set to generate samples that are completely outside the support of the original training distribution; this phenomenon leads diffusion models to generate artifacts that never existed in real data (i.e., hallucinations). We systematically study the reasons for, and the manifestation of this phenomenon.

A comprehensive benchmark is yet to be established in the Image Manipulation Detection & Localization (IMDL) field. The absence of such a benchmark leads to insufficient and misleading model evaluations, severely undermining the development of this field. However, the scarcity of open-sourced baseline models and inconsistent training and evaluation protocols make conducting rigorous experiments and faithful comparisons among IMDL models challenging. To address these challenges, we introduce IMDL-BenCo, the first comprehensive IMDL benchmark and modular codebase. IMDL-BenCo: i) decomposes the IMDL framework into standardized, reusable components and revises the model construction pipeline, improving coding efficiency and customization flexibility; ii) fully implements or incorporates training code for state-of-the-art models to establish a comprehensive IMDL benchmark; and iii) conducts deep analysis based on the established benchmark and codebase, offering new insights into IMDL model architecture, dataset characteristics, and evaluation standards. Specifically, IMDL-BenCo includes common processing algorithms, 8 state-of-the-art IMDL models (1 of which are reproduced from scratch), 2 sets of standard training and evaluation protocols, 15 GPU-accelerated evaluation metrics, and 3 kinds of robustness evaluation. This benchmark and codebase represent a significant leap forward in calibrating the current progress in the IMDL field and inspiring future breakthroughs.

In reinforcement learning (RL), it is common to apply techniques used broadly in machine learning such as neural network function approximators and momentumbased optimizers [1, 2]. However, such tools were largely developed for supervised learning rather than nonstationary RL, leading practitioners to adopt target networks [3], clipped policy updates [4], and other RL-specific implementation tricks [5, 6] to combat this mismatch, rather than directly adapting this toolchain for use in RL. In this paper, we take a different approach and instead address the effect of nonstationarity by adapting the widely used Adam optimiser [7]. We first analyse the impact of nonstationary gradient magnitude--such as that caused by a change in target network--on Adam's update size, demonstrating that such a change can lead to large updates and hence sub-optimal performance. To address this, we introduce Adam with Relative Timesteps, or Adam-Rel. Rather than using the global timestep in the Adam update, Adam-Rel uses the local timestep within an epoch, essentially resetting Adam's timestep to 0 after target changes. We demonstrate that this avoids large updates and reduces to learning rate annealing in the absence of such increases in gradient magnitude. Evaluating Adam-Rel in both on-policy and off-policy RL, we demonstrate improved performance in both Atari and Craftax. We then show that increases in gradient norm occur in RL in practice, and examine the differences between our theoretical model and the observed data.

Softmax attention is the principle backbone of foundation models for various artificial intelligence applications, yet its quadratic complexity in sequence length can limit its inference throughput in long-context settings. To address this challenge, alternative architectures such as linear attention, State Space Models (SSMs), and Recurrent Neural Networks (RNNs) have been considered as more efficient alternatives. While connections between these approaches exist, such models are commonly developed in isolation and there is a lack of theoretical understanding of the shared principles underpinning these architectures and their subtle differences, greatly influencing performance and scalability. In this paper, we introduce the Dynamical Systems Framework (DSF), which allows a principled investigation of all these architectures in a common representation.

With the widespread application of Large Language Models (LLMs) to various domains, concerns regarding the trustworthiness of LLMs in safety-critical scenarios have been raised, due to their unpredictable tendency to hallucinate and generate misinformation. Existing LLMs do not have an inherent functionality to provide the users with an uncertainty/confidence metric for each response it generates, making it difficult to evaluate trustworthiness. Although several studies aim to develop uncertainty quantification methods for LLMs, they have fundamental limitations, such as being restricted to classification tasks, requiring additional training and data, considering only lexical instead of semantic information, and being prompt-wise but not response-wise. A new framework is proposed in this paper to address these issues.

For what purpose was the dataset created? Was there a specific task in mind? This work is partially funded by Cisco and Amazon. Are there multiple types of instances (e.g. Each scenario essentially contains a user's LLM's generated program conforms to the user's intent.